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Spatial transcriptome constructing method

A technology of spatial transcription and construction methods, applied in the fields of biochemical equipment and methods, genomics, proteomics, etc., can solve the problems of complex experimental operation, achieve a wide range of applications, speed up analysis, reduce costs and operational complexity Effect

Pending Publication Date: 2020-09-18
SOUTHEAST UNIV
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Problems solved by technology

Such methods rely heavily on the information used for landmark genes, which are different in different tissues, and the experimental operations are relatively complex

Method used

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Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0042] Construction of a spatial location map of adult cardiac tissue.

[0043] 1. Obtain images of adult heart tissue slices

[0044] Determine the tissue samples, select tissue samples with clear outlines to take pictures, and generate tissue slice pictures (see figure 2 ).

[0045] 2. Microplot Sampling Cells

[0046] Single cells are collected from different regions in tissue sections, and single-cell RNA sequencing (ie, single-cell cytoplasmic mRNA sequencing) is performed on the sampled cells, and the gene expression data and location information of the sampling points are recorded.

[0047] 3. Determination of single-cell expression data in adult heart tissue

[0048]Using single-cell RNA sequencing technology (i.e., single-cell cytoplasmic mRNA sequencing) to measure the transcriptome data of all cells in adult heart tissue samples, the raw data are compared to obtain the expression levels of all genes in each cell.

[0049] 4. Data preprocessing

[0050] Express...

Embodiment 2

[0059] Construction of spatial location map of mouse hippocampus.

[0060] 1. Obtain pictures of mouse hippocampal tissue slices

[0061] Determine tissue samples, select tissue samples with clear outlines and take pictures, and generate tissue slice pictures.

[0062] 2. Microplot Sampling Cells

[0063] Cells were collected from different areas in the tissue section, and single-nuclear RNA sequencing was performed on the sampled cells, and the nuclear gene expression data and location information of the sampling points were recorded.

[0064] 3. Determination of single-nucleus gene expression data of mouse hippocampus tissue

[0065] Single-nucleus RNA sequencing technology was used to measure the single-cell transcriptome data of all cells in the mouse hippocampus tissue sample, and the original data were compared to obtain the expression of all genes in each nucleus.

[0066] 4. Data preprocessing

[0067] Expression Data Extract raw gene expression data, import the fi...

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Abstract

The invention provides a spatial transcriptome constructing method. The method comprises the steps as follows: firstly, sampling a single cell at a local spatial position of a sample by a micro-regionsampling technology and sequencing the transcriptome; then, obtaining transcriptome information of each cell of the sample by a single cell sequencing method; and finally, constructing spatial positions of all the cells in the sample according to the characteristics of similar gene expression of adjacent cells, based on transcriptome sequencing data of the local spatial position of the cell as areference system, so as to obtain spatial transcriptome information of the whole tissue. The method is not only suitable for cytoplasmic transcriptome data, but also suitable for nuclear transcriptomedata, can effectively reduce the construction cost of the spatial transcriptome. The spatial transcriptome constructing method can be widely applied to spatial cell map drawing, so that technical support is provided for research of tumor microenvironment heterogeneity analysis, brain spatial neural network map construction and the like.

Description

technical field [0001] The present invention proposes a method for constructing single-cell spatial location and single-cell transcriptional profile by using tissue sample cell transcriptome information, which belongs to the field of single-cell spatial omics analysis, and can be applied to researches such as tumor microenvironment and neural network identification. Background technique [0002] The spatial location information and transcriptome information of single cells in tissues are crucial for analyzing the cancer microenvironment and constructing neural network circuits. However, the current single-cell analysis method will lose the spatial position information of the cell while obtaining the cell transcriptome information; moreover, the sample must be a fresh sample, and only cytoplasmic RNA molecules can be measured. Developing a single-cell transcriptome analysis method that is applicable to both cell mass and nuclear transcriptome, and simultaneously obtains the s...

Claims

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Application Information

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IPC IPC(8): C12Q1/6869G06T7/11G06T11/40G16B20/30
CPCC12Q1/6869G16B20/30G06T7/11G06T11/40
Inventor 赵祥伟刘宏德陈正葛芹玉
Owner SOUTHEAST UNIV
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